When you ran chkdsk you were running DOS or Windows. This means that a
code-page is set for the operating system at that time. When you insert
a USB disk, it is also running under that code-page. When you then run
chkdsk it checks characters based on the current code-page.

It has just occurred to me that until now I did not actually have access
to a file-system that has "bad characters" on it and is by the look of
things from a Non-US code-page. So, if you are in fact running a Non-US
version of DOS/Windows, I'd appreciate it if you could create a dd-image
of a small USB thumb-drive with some "bad characters" on it, so I could
attempt some more testing.

-- 
Problem in FSCK checking Chinese filename (Big5)
https://bugs.launchpad.net/bugs/49217
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